MolNFT v1 · #66138 · protein
Crystal structure of methylated RPA0582 protein
3HHL: “Crystal structure of methylated RPA0582 protein”. X-ray diffraction, 2 ligands (CL, SO4), 6 pockets (best druggability 0.68). MolNFT v1 #66138 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HHL
- Type
- protein
- Length
- 540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RPA0582
- UniProt
- Q6NC90
- Ligands
- CL, SO4
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RPA0582 | protein | 135 | 36% helix, 31% strand | Q6NC90 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 3 copies · chains A, D, B, C
- 2PE · Nonaethylene glycol · additive · 2 copies · chains A, D
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · 2 copies · chains B, C
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, C, A, D
- 1PE · Pentaethylene glycol · additive · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.68 | 0.83 | 31 | CL, PE8 |
| 2 | 278 | 0.67 | 0.82 | 39 | CL, 2PE |
| 3 | 271 | 0.66 | 0.82 | 35 | CL, 2PE |
| 4 | 261 | 0.66 | 0.82 | 36 | CL, PE8 |
| 5 | 126 | 0.42 | 0.76 | 17 | SO4 |
Interfaces
3 interfaces between chains.
- B–C · 2298 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 2281 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 412 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered, methylation).
Compared structures
- 3HHL · Crystal structure of methylated RPA0582 protein · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q6NC90
- Elsewhere: RCSB PDB 3HHL · PDBe 3HHL · UniProt Q6NC90
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